The ending of IV. In the end, you save everyone, even Baldur, and while the Medium can't just magic away the fertility problems the Empire is having and that may someday threaten Tharsis, the entire tone of the ending is "you know, if we just cooperate and pool our knowledge, we can probably find an answer". You then see the transformed, cosmopolitan, newly-multiracial Tharsis through the eyes of a new set of adventurers, and see that all your friends are okay (and are talking the player guild up), ending with "Whirlwind" (in his old getup and everything!) showing the new kids the ropes just like he did for you. All while this song is playing.
Also in IV, despite Wufan showing disdain for humans and Logre/Whirlwind "betraying" you, you can choose to forgive them by choosing the "wordlessly extend your hand" option. So moved by your kindness, they join you as a guest - and then can become permanent members of your guild later on!
The Outlands Count looks ridiculous in his pampered getup and fluffy lapdog. However, he's a very active member of Tharsis' government, pledges the city resources to helping the Vessels and the Sentinels when informed of their plight, and when The Empire barges in and starts making demands, he makes it very clear Tharsis comes ahead of him. The Imperials can threaten him all they like - as far as he's concerned, he's expendable compared to the city and those under its protection.
Beyond the Myth has the Animal Care skill available for some races; it allows the user to take care of livestock, resulting in some rather cute field events:
In the first stratum, you can catch a chicken, who then stays at the inn and occasionally rewards your patience with eggs.
In the second stratum, you can feed a hen with some Forest Fish to help it recover its stamina and fly off. You then see the same hen appear several more times throughout the stratum, and each time you help it out again the same way. Turns into a Funny Moment when it starts following you and you leave it at the inn...only for it to offer fish by spitting it out.
Also in Beyond the Myth, you can feed a dog in the third Stratum. On a later floor, you will encounter a zombie dog that turns out to be the same dog from before, mourning its deceased Master. If you spare this dog, that retains its sense of self despite being rendered undead, it will give you some of its late Master's money.